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Magnesium in PDB 1t8q: Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli

Enzymatic activity of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli

All present enzymatic activity of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli:
3.1.4.46;

Protein crystallography data

The structure of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli, PDB code: 1t8q was solved by R.Zhang, Y.Kim, I.Dementieva, N.Duke, L.Stols, M.Donnelly, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.56 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.759, 118.386, 242.048, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 26.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli (pdb code 1t8q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli, PDB code: 1t8q:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1t8q

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Magnesium binding site 1 out of 4 in the Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:27.3
occ:1.00
 OE1 A:GLU171 2.1 20.9 1.0
OE1 A:GLU63 2.2 32.0 1.0
O3 A:GOL1605 2.3 28.5 1.0
O1 A:GOL1605 2.3 29.8 1.0
OD1 A:ASP65 2.4 20.9 1.0
O A:HOH1615 2.4 21.9 1.0
CD A:GLU171 3.2 17.8 1.0
CD A:GLU63 3.3 35.5 1.0
CG A:ASP65 3.3 25.3 1.0
C3 A:GOL1605 3.3 33.2 1.0
C1 A:GOL1605 3.4 32.3 1.0
OD2 A:ASP65 3.4 19.1 1.0
OE2 A:GLU63 3.6 35.1 1.0
C2 A:GOL1605 3.7 32.5 1.0
OE2 A:GLU171 4.0 18.9 1.0
O2 A:GOL1605 4.0 33.2 1.0
CB A:GLU171 4.0 24.1 1.0
O A:HOH1657 4.1 31.2 1.0
NE2 A:HIS36 4.1 22.4 1.0
CG A:GLU171 4.2 23.9 1.0
NE2 A:GLN208 4.3 33.2 1.0
CD2 A:HIS36 4.4 27.4 1.0
O A:HOH1616 4.5 27.0 1.0
CG A:GLU63 4.6 32.0 1.0
CB A:ASP65 4.6 22.2 1.0
NE A:ARG37 4.8 24.6 1.0
CD A:GLN208 4.9 31.8 1.0
NZ A:LYS173 4.9 19.3 1.0
O A:GLN64 5.0 24.6 1.0

Magnesium binding site 2 out of 4 in 1t8q

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Magnesium binding site 2 out of 4 in the Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1602

b:22.8
occ:1.00
 OE1 B:GLU171 2.2 21.4 1.0
O3 B:GOL1606 2.3 26.4 1.0
O1 B:GOL1606 2.3 23.2 1.0
OD1 B:ASP65 2.3 23.0 1.0
OE1 B:GLU63 2.3 22.3 1.0
O B:HOH1612 2.3 19.9 1.0
CG B:ASP65 3.2 22.3 1.0
CD B:GLU63 3.2 23.2 1.0
CD B:GLU171 3.2 21.4 1.0
C1 B:GOL1606 3.3 26.9 1.0
OD2 B:ASP65 3.3 20.3 1.0
C3 B:GOL1606 3.4 29.3 1.0
OE2 B:GLU63 3.5 22.5 1.0
C2 B:GOL1606 3.7 28.0 1.0
OE2 B:GLU171 3.9 20.8 1.0
CB B:GLU171 4.0 22.1 1.0
O2 B:GOL1606 4.1 28.5 1.0
O B:HOH1613 4.1 27.7 1.0
NE2 B:HIS36 4.2 22.3 1.0
CG B:GLU171 4.2 21.8 1.0
NE2 B:GLN208 4.4 28.2 1.0
O B:HOH1677 4.5 25.1 1.0
CG B:GLU63 4.5 20.0 1.0
CB B:ASP65 4.6 21.0 1.0
CD2 B:HIS36 4.6 20.5 1.0
NZ B:LYS173 4.8 17.4 1.0
NE B:ARG37 4.8 20.1 1.0
O B:GLN64 4.9 25.6 1.0
CD B:GLN208 4.9 28.9 1.0
CD B:LYS173 5.0 18.4 1.0
CA B:ASP65 5.0 21.8 1.0

Magnesium binding site 3 out of 4 in 1t8q

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Magnesium binding site 3 out of 4 in the Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1603

b:29.4
occ:1.00
 OE1 C:GLU171 2.3 30.1 1.0
OE1 C:GLU63 2.3 38.5 1.0
OD1 C:ASP65 2.3 26.1 1.0
O C:HOH1614 2.3 35.1 1.0
O1 C:GOL1607 2.3 33.7 1.0
O3 C:GOL1607 2.4 38.5 1.0
CG C:ASP65 3.1 27.4 1.0
CD C:GLU63 3.2 36.3 1.0
OD2 C:ASP65 3.2 28.2 1.0
CD C:GLU171 3.4 29.4 1.0
OE2 C:GLU63 3.5 36.0 1.0
C1 C:GOL1607 3.5 35.9 1.0
C3 C:GOL1607 3.5 37.1 1.0
C2 C:GOL1607 3.9 35.4 1.0
O2 C:GOL1607 4.0 36.3 1.0
OE2 C:GLU171 4.0 32.4 1.0
O C:HOH1653 4.2 25.4 1.0
O C:HOH1739 4.2 41.3 1.0
CB C:GLU171 4.3 28.6 1.0
NE2 C:HIS36 4.3 30.1 1.0
CG C:GLU171 4.4 31.1 1.0
NE2 C:GLN208 4.5 35.8 1.0
CB C:ASP65 4.6 27.5 1.0
CG C:GLU63 4.6 34.5 1.0
CD2 C:HIS36 4.6 31.6 1.0
NE C:ARG37 4.7 29.0 1.0
NH2 C:ARG37 4.8 29.1 1.0
O C:GLN64 4.9 28.9 1.0
NZ C:LYS173 5.0 34.0 1.0

Magnesium binding site 4 out of 4 in 1t8q

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Magnesium binding site 4 out of 4 in the Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1604

b:35.4
occ:1.00
 OE1 D:GLU63 2.2 40.1 1.0
OD1 D:ASP65 2.2 33.5 1.0
O1 D:GOL1608 2.3 38.4 1.0
O D:HOH1616 2.3 34.2 1.0
OE1 D:GLU171 2.3 38.0 1.0
O3 D:GOL1608 2.3 41.3 1.0
CD D:GLU63 3.1 38.3 1.0
CG D:ASP65 3.2 33.8 1.0
CD D:GLU171 3.3 37.3 1.0
C3 D:GOL1608 3.3 42.9 1.0
C1 D:GOL1608 3.4 42.5 1.0
OD2 D:ASP65 3.4 34.3 1.0
OE2 D:GLU63 3.6 38.4 1.0
C2 D:GOL1608 3.8 41.8 1.0
CB D:GLU171 4.0 35.1 1.0
OE2 D:GLU171 4.0 36.3 1.0
O2 D:GOL1608 4.0 42.3 1.0
O D:HOH1746 4.2 53.3 1.0
NE2 D:HIS36 4.2 37.1 1.0
CG D:GLU171 4.2 37.1 1.0
NE2 D:GLN208 4.3 44.8 1.0
CG D:GLU63 4.3 38.0 1.0
O D:HOH1639 4.5 45.3 1.0
CB D:ASP65 4.5 32.7 1.0
CD2 D:HIS36 4.6 37.7 1.0
O D:GLN64 4.7 34.9 1.0
CD D:GLN208 4.8 45.2 1.0
NE D:ARG37 4.9 40.2 1.0
CA D:ASP65 4.9 31.9 1.0
CD D:LYS173 5.0 31.6 1.0

Reference:

R.Zhang, Y.Kim, I.Dementieva, N.Duke, L.Stols, M.Donnelly, A.Joachimiak. The Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli To Be Published.
Page generated: Sun Aug 10 04:49:58 2025

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